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The diagnosis of bacterial diseases in clinical microbiology has relied on phenotypic identification, based on the bacterial repertoire known to be associated with humans. This mode of identification, which is, [...]

Abstract Introduction Haemophilus pittmaniae was described in 2005 as a new species distantly related to Haemophilus parainfluenzae. This member of the human saliva microbiota has also been further isolated from various body fluids without formal description of the patients. Case presentation We report the case of H. pittmaniae isolate made from a sputum specimen collected from a 58-year-old Caucasian man with a massive fibrotic form of siderosis who was awaiting lung transplantation. Identification of the isolate was ascertained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene sequencing. H. pittmaniae was considered to be responsible for the worsening of the patient’s chronic respiratory failure and was successfully treated with oral amoxicillin. Conclusion H. pittmaniae should be regarded as a new pathogen responsible for respiratory tract infection in patients with chronic lung diseases.

Background: Non-tuberculous mycobacteria recovered from respiratory tract specimens are emerging confounder organisms for the laboratory diagnosis of tuberculosis worldwide. There is an urgent need for new techniques to rapidly identify mycobacteria isolated in clinical practice. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDITOF MS) has previously been proven to effectively identify mycobacteria grown in high-concentration inocula from collections. However, a thorough evaluation of its use in routine laboratory practice has not been performed. Methodology: We set up an original protocol for the MALDI-TOF MS identification of heat-inactivated mycobacteria after dissociation in Tween-20, mechanical breaking of the cell wall and protein extraction with formic acid and acetonitrile. By applying this protocol to as few as 105 colony-forming units of reference isolates of Mycobacterium tuberculosis, Mycobacterium avium, and 20 other Mycobacterium species, we obtained species-specific mass spectra for the creation of a local database. Using this database, our protocol enabled the identification by MALDI-TOF MS of 87 M. tuberculosis, 25 M. avium and 12 non-tuberculosis clinical isolates with identification scores ≥2 within 2.5 hours. Conclusions: Our data indicate that MALDI-TOF MS can be used as a first-line method for the routine identification of heatinactivated mycobacteria. MALDI-TOF MS is an attractive method for implementation in clinical microbiology laboratories in both developed and developing countries [ABSTRACT FROM AUTHOR]

Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1 T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C 15:0 anteiso (36%), C 16:0 (19%), and C 15:0 iso (10%). Based on an analysis of the full-length 16S rRNA gene sequences, phylogenetic analysis showed that the strain khD1 T exhibited 90% sequence similarity with Prevotella loescheii, the phylogenetically closest validated Prevotella species. With 3,763,057 bp length, the genome of strain khD1 T contained (mol%) 48.7 G + C and 3248 predicted genes, including 3194 protein-coding and 54 RNA genes. Given the phenotypical and biochemical characteristic results as well as genome sequencing, strain khD1 T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella lascolaii sp. nov. is proposed. The type strain is khD1 T ( = CSUR P0109, = DSM 101754). These results show that microbial culturomics greatly improves the characterization of the human microbiome repertoire by isolating potential putative new species. Further studies will certainly clarify the microbial mechanisms of pathogenesis of these new microbes and their role in health and disease. Microbial culturomics is an important new addition to the diagnostic medicine toolbox and warrants attention in future medical, global health, and integrative biology postgraduate teaching curricula.

Strain SIT6 T was isolated from the fecal flora of a severely malnourished child as part of a broad "culturomics" study aiming to maximize the culture conditions for the in-depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6 T shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKP T (NR_029151), the phylogenetically closest type species. Colonies are creamy white, circular, 4-5 mm in diameter after cultivation at 37°C for 24 hr on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 25-56°C (optimally at 37°C). Strain SIT6 T is a gram-positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637-bp-long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein-coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA-DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6 T against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6 T (=CSUR P2452 T , =DSM 29059 T )., (© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Background: Pasteurella multocida meningitis in an immunocompetent patient is rare and commonly occurs after animal bite. To our knowledge, only 48 cases have been reported in the literature since 1989. P. multocida meningitis is commonly linked to animal contagion. Here we report on a new case of P. multocida meningitis in an immunocompetent patient who is a dog owner without a dog bite. We used the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to investigate the clonal lineage between animal and human isolates., Case Presentation: In our case, a 25-year-old immunocompetent French Caucasian woman with nothing notable in her medical history was admitted for meningitis caused by P. multocida. Clonal lineage of P. multocida strains from cerebrospinal fluid and blood culture and her dog's oral cavity has been recognized by MALDI-TOF mass spectrometry dendrograms and clustering of the 21 P. multocida isolates in our centres. She was treated by a combination of intravenous ceftriaxone (2 g/day) and oral levofloxacin (1 g/day). She was discharged on the 6th day of admission. The antimicrobial therapy was conducted for 15 days. The dog was treated by clavulanic-acid amoxicillin for 3 weeks by the veterinarian. The evolution of the patient at the 5th month after the end of the antimicrobial therapy was normal without any neurological after-effects., Conclusion: The meningitis caused by P. multocida could be considered a cause of human meningitis in dog lovers without an animal bite. MALDI-TOF mass spectrometry should be considered as it is an accurate tool to identify clonal lineage between animal and human isolates.